Personal acknowledgements

This thesis would not have been possible without the tremendous support I have been so incredibly lucky to get from my closest and dearest throughout my PhD journey.

First of all I must thank my wonderful and amazing wife Gaby. You are my strongest pillar, making me motivated and focused, supporting me even when I have been difficult or absent-minded. I could not have done this without your love, and I am forever grateful. ¡Te amo con todo mi corazón!

Much of my daily joy comes from the my children, and I am glad for all the time we have together – including during COVID-19 lockdown when work, study and life mixed all up! (apologies to readers if you find any Odd Squad references). You will probably insist I also thank Waldo – OK, he has also been there, although mostly sleeping in his little corner!

I want to thank my family in Norway – specially my parents who have been encouraging me throughout, and my siblings and cousins who always make it a pleasure to “come home” and give me regular updates. Thank you to all my friends, in particular Laura, Juan, Ian, Sverre, Erlend, and Magnus.

I am forever in debt to Paul Groth and I want to thank you for agreeing to supervise me as your PhD student, which must have been challenging at the best of times. I have enjoyed working with you since we first started talking about provenance and workflows more than a decade ago! Thank you for all your patience, persistence and for your pragmatic directions that kept me on track. Thanks also to the INDE lab at University of Amsterdam, particularly for the daily colleaguality we got during lockdown – I wish I could have spent more time with you in person!

Thank you to Carole Goble, you have always been supporting me in so many ways since I started working for you in 2006, and you convinced me to start this PhD in the first place! No wonder you kept asking if I was finished yet! I appreciate our friendship and how you have mentored me to grow from a geeky developer to an acedemic. I hope we continue our exciting collaborations as “proper” colleagues!

I am so happy to have worked at the eScience Lab at The University of Manchester for all these years and during this PhD. I particularly want to thank Shoaib Sufi for your wisdom and our deep conversations, not to mention your reliability whenever I have been stunned by bureaucracy or other struggles – I’ve probably been the oddest person for you to line manage! Thank you to all my amazing colleagues at the eScience Lab – specially Stuart, Finn, Alex, Nick, Munazah, Alan – you are a pleasure to work with, not just for your skills and expertise, but also your friendship and support.

I want to thank Meznah, you have been in the odd position of being co-supervised by me for your own PhD, and at the same time pushing me to finish mine! You bring such a joy with everything you do! Thanks to my fellow PhD and EngD students in Manchester: Fuqi, Ebitsam, Yo – you inspire me! Thanks to Rudolf Wittner, your productive provenance visits to Manchester have hopefully helped your PhD as much as mine!

I also want to thank Andrew Stewart, Uli Sattler and the rest of Department of Computer Science, who have been so accommodating, and you are now welcoming me again as I step into the academic world fully. It’s not like you didn’t prepare me! I also want to thank the UCU union members in Manchester (UMUCU) – particularly Bijan and Ben for their personal support. I may have lost track of how many times we’ve been on the picket line during this PhD (no, I didn’t manage to do much writing on strike days), but you have also showed me not to give up! Thank you to the engaging University of Manchester Students' Union, for standing up for what is right!

Community acknowledgements

I am grateful for all the wonderful discussions, technical contributrions and long-lasting friendships formed in the RO-Crate community (listed ) since its early inception [@Ó; @Carragáin; @2019a] at Workshop on Research Objects (RO2018). Without you there would not have been any RO-Crate!

I would particularly like to thank Peter Sefton, without which co-chairing, enthusiasm and pragmatism I would easily had got lost the weeds. I am forever in debt to Eoghan Ó Carragáin who managed to get me and Peter to agree even on the trickiest issues, and led the community through its formative years.

I want to thank Simone Leo, which persistent work and leadership on Workflow Run Crate and the RO-Crate Python library [@De; @Geest; @2023a] has shown that RO-Crate works in practice even for detailed provenance.

Thank you to Bruno Kinoshita who kindly (and on own initiative) helped proof this whole thesis, you have contributed to our common goals in so many ways, going back to when we first worked on Semantic Web, Apache Jena, and Common Workflow Language and later RO-Crate.

I am very grateful to Daniel Garijo, with whom I have enjoyed many insightful discussions and idea developments for more than a decade (since the early days of Research Objects!), from the cellar of Dagstuhl to beaches of San Diego! I appreciate your enthusiasm and many invaluable and constructive contributions to manuscripts, specifications and code.

I want to thank Leyla Jael Castro, for your continuous positivity and drive, and for pushing us to run RO-Crate training workshops together with Núria Queralt Rosinach and Claus Weiland. I always appreciate our discussions and writing together, and I am so glad that you are much better than me to remember submission deadlines!

RO-Crate is standing on the shoulders of giants, and I would like to thank the whole Research Object community [@Goble; @2018] for persisting on the early RO ideas [@Newman; @2009; @Bechhofer; @2013]. I have particular fond memories of whiteboard sessions with Sean Bechhofer, Khalid Belhajjame, Paolo Missier, David De Roure, and Kevin Page in the productive Wf4Ever project that laid the foundation for what is now RO-Crate.

This PhD is in many ways born out of ELIXIR Europe, not just through its many fruitful co-author contributions (section B.1), but also as the “ELIXIR way” of working is emblematic for the approach taken by RO-Crate community: open collaborations where institutional and project boundaries are blurred out in favour of jointly building pragmatic solutions.

I would like to thank the lovely people of ELIXIR Belgium (incl. Frederik, Ignacio, Paul, Rafael, Bert), ELIXIR Spain (incl. José Mª, Laura, Salva, Adam, Pau), ELIXIR HUB (incl. Justin, Jonathan, Marieke, Gavin, Niklas, Katharina), ELIXIR DE (incl. Björn, Anika, Sebastian, Nils, Michael), ELIXIR CH (Alex, Patricia), ELIXIR UK (incl. Susanna, Nicola, Xenia, Tim, Neil), ELIXIR NL (Núria, Egon, Chris, Marco, Rob, Helena) and many others I may have missed listing. I want to particularly thank everyone who organized and participated in the ELIXIR Biohackathons which always inspires me and has helped build our communities.

This thesis frequently mentions the Common Workflow Language[^1], and many of the ideas spur out of methods that were first tried by the CWL community (see for example [@Möller; @2017; @Robinson; @2017; @Khan; @2019; @Crusoe; @2022]), which I am grateful for. I want to thank Michael Crusoe, not just for your tiredless work on bringing CWL together and willingness to put FAIR workflow theories into practice, but also for our enduring friendship and your support throughout most of the rabbit holes I’ve ventured into. I want to thank Peter Amstutz, Hervé Ménager and the rest of the CWL leadership team and the many volunteers.

I also need to thank members of the BioCompute Object community, particularly Hadley, Jonathon, Raja, Dennis, Vahan, Janisha, Amanda, and Nicola. I thank the Workflows Community Initiative in particular Sean R. Wilkinson, Rafael Ferreira da Silva, and Kyle Chard.

From the FAIR Digital Object Forum I need to place particular thanks to Peter Wittenburg, Luiz Olavo Bonino da Silva Santos, Maggie Hellström, Ulrich Schwardmann and Rainer Stotzka. I also want to thank all the members of the the Research Data Alliance’s FAIR Digital Object Fabric interest group.

Mark Wilkinson, we first worked together on BioMoby services and Taverna workflows, which seems a long way from where we are today with FAIR! Looking back from this thesis, perhaps we could consider those to be early FAIR digital objects as well? I want to thank you for your enthusiasm, and for bringing me in to the Apples2Apples hackathons – thank you also to Robert, Richard, Wilko, David, Alban, and Allyson.

Thank you to Egon Willighagen, I always enjoy our conversations, be it in the wind at Zandvoort, at the warmth of a Biohackathon cabin, or at Mastodon. I am indebted for your help and your Dutch expertise!

I am indebted to Herbert van de Sompel – our conversations on the topic of aggregations, annotations, mementos and the Web started more than a decade ago; your clear ideas and powerful visions are at the heart of what this thesis tries to achieve. I am always energised by your talks, and truly appreciate working with you to promote FAIR Signposting and hope we will continue such exciting work together.

RO-Crate Community

As of 2024-01-08, the RO-Crate Community members are:

In remembrance

I am saddened by the loss of Olav S. Bratli, Stu Allan, James Taylor, Sarah Jones, Henry Story, Chris Connolly, Lloyd Cawthorne, and other such brilliant and lovely people.

In memoriam: Damon Harvey, Luke O’Connor, Cian Chantrill, Brianna Ghey, Ben Trueman, Ryan Watson, Finn Kitson, Rory Wood, William King, Harrison De George, Charlotte Burlace-Colquhoun, Finn Kitson, Charley Gadd, Sumanta Bansi, Rhys Hill, Laura Nuttall and other students whose lives were cut too short.

My thoughts are with the victims of war, conflict, crime and abuse in Ukraine, Palestine, Israel, Yemen, Sudan, Mexico and across the world.

My funding

My work presented in this thesis has been undertaken during several research projects at The University of Manchester, which funding is acknowledged below:

Where indicated both EU Grant and UKRI, funding from UK Research and Innovation were granted under the UK government’s Horizon Europe funding guarantee.

Funding and acknowledgements for co-authored chapters

Acknowledgements for Evaluating FAIR Digital Object and Linked Data as distributed object systems

Chapter 2 and section 3.1 are adapted from an journal article accepted for publication in PeerJ Computer Science.

Published as preprint

Stian Soiland-Reyes, Carole Goble, Paul Groth (2023):
Evaluating FAIR Digital Object and Linked Data as distributed object systems.
arXiv 2306.07436 [cs.DC]
https://doi.org/10.48550/arXiv.2306.07436

An RO-Crate for this article is archived in Zenodo: https://doi.org/10.5281/zenodo.8075229

Acknowledgements

We would like to acknowledge the FAIR Digital Object Forum community and working groups, where SSR and CG are members.

Views and opinions expressed in this work are those of the authors only and do not necessarily reflect those of the funded projects, FAIR Digital Object Forum, European Union nor the European Commission.

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Minor LaTeX changes; references in s11 house style; citations merged and renumbered; funding and references moved to separate chapters. Background copied to separate chapter. Added footnote to define machine actionable, added figures fdo, jsonld and listing triples. Minor typos and grammatical errors fixed.

Funding

This work was funded by the European Union programmes Horizon 2020 under grant agreements H2020-INFRAEDI-02-2018 823830 (BioExcel-2), H2020-INFRAEOSC-2018-2 824087 (EOSC-Life) and Horizon Europe under grant agreements HORIZON-INFRA-2021-EMERGENCY-01 101046203 (BY-COVID), HORIZON-INFRA-2021-EOSC-01 101057388 (EuroScienceGateway), HORIZON-INFRA-2021-EOSC-01-05 101057344 (FAIR-IMPACT), HORIZON-INFRA-2021-TECH-01 101057437 (BioDT), HORIZON-CL4-2021-HUMAN-01-01 101070305 (ENEXA); and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grants 10038963 (EuroScienceGateway), 10038992 (FAIR-IMPACT), 10038930 (BioDT).

Views and opinions expressed in this work are those of the authors only and do not necessarily reflect those of the funded projects, FAIR Digital Object Forum, European Union nor the European Commission.

Acknowledgements for Updating Linked Data practices for FAIR Digital Object principles

Section 3.2 is adapted from a published peer-reviewed conference abstract, presented as talk by Stian Soiland-Reyes at First International Conference on FAIR Digital Objects (FDO2022) on 2022-08-26/–28 in Leiden, The Netherlands.

• Slides: https://doi.org/10.5281/zenodo.7256428

Published As

Stian Soiland-Reyes, Leyla Jael Castro, Daniel Garijo, Marc Portier, Carole Goble, Paul Groth (2022):
Updating Linked Data practices for FAIR Digital Object principles.
1st International Conference on FAIR Digital Objects (FDO 2022) (abstract).
Research Ideas and Outcomes 8:e94501
https://doi.org/10.3897/rio.8.e94501

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Formatting as Markdown and LaTeX; figure caption formatting; reference in s11 house style; citations merged and renumbered; new introduction; acknowledgements and references moved to separate chapters.

Acknowledgements

We would like to acknowledge the RO-Crate community and the WorkflowHub Club. Thanks to Rudolf Wittner for valuable comments.

Funding

European Commission Horizon 2020 (EOSC-Life 824087), Horizon Europe (BY-COVID 101046203, FAIR-IMPACT 101057344).

Leyla Jael Castro is supported by a German Research Foundation DFG grant for NFDI4DataScience.

Daniel Garijo is supported by the Madrid Government (Comunidad de Madrid-Spain) under the Multiannual Agreement with Universidad Politécnica de Madrid in the line Support for R&D projects for Beatriz Galindo researchers, in the context of the V PRICIT (Regional Programme of Research and Technological Innovation)

Acknowledgements for Packaging research artefacts with RO-Crate

Section 4.1 and section 4.3 are adapted from an article published in the journal Data Science.

Published As

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022):
Packaging research artefacts with RO-Crate.
Data Science 5(2)
https://doi.org/10.3233/DS-210053

An RO-Crate for this article is archived at https://doi.org/10.5281/zenodo.5146227

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Formatting as Markdown and LaTeX; figure caption formatting; reference in s11 house style; added identifiers, authors and years clarified where missing in citations; inline citation hyperlinks to open access version where available; citations merged and renumbered; acknowledgements and references moved to separate chapters; fixed minor typos and grammatical errors.

Funding

This work has received funding from the European Commission’s Horizon 2020 research and innovation programme for projects BioExcel-2 (H2020-INFRAEDI-2018-1 823830), IBISBA 1.0 (H2020-INFRAIA-2017-1-two-stage 730976), PREP-IBISBA (H2020-INFRADEV-2019-2 871118), EOSC-Life (H2020-INFRAEOSC-2018-2 824087), SyntheSys+ (H2020-INFRAIA-2018-1 823827). From the Horizon Europe Framework Programme this work has received funding for BY-COVID (HORIZON-INFRA-2021-EMERGENCY-01 101046203).

Björn Grüning is supported by DataPLANT (NFDI 7/1 – 42077441), part of the German National Research Data Infrastructure (NFDI), funded by the Deutsche Forschungsgemeinschaft (DFG).

Ana Trisovic is funded by the Alfred P. Sloan Foundation (grant number P-2020-13988). Harvard Data Commons is supported by an award from Harvard University Information Technology (HUIT).

Acknowledgements for Creating lightweight FAIR Digital Objects with RO-Crate

Section 4.2 is adapted from a published peer-reviewed conference abstract, presented as poster by Stian Soiland-Reyes at First International Conference on FAIR Digital Objects (FDO2022) on 022-08-26/–28 in Leiden, The Netherlands.

• Poster: https://doi.org/10.5281/zenodo.7245315

Published As

Stian Soiland-Reyes, Peter Sefton, Leyla Jael Castro, Frederik Coppens, Daniel Garijo, Simone Leo, Marc Portier, Paul Groth (2022):
Creating lightweight FAIR Digital Objects with RO-Crate.
1st International Conference on FAIR Digital Objects (FDO2022) (poster)
Research Ideas and Outcomes 8:e93937
https://doi.org/10.3897/rio.8.e93937

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Formatting as Markdown and LaTeX; figure caption formatting; references in s11 house style; citations merged and renumbered; acknowledgements and references moved to separate chapters. Figure signposting font re-rendered. Added figure signposting. Fixed minor typos and grammatical errors.

Acknowledgements

We would like to acknowledge the RO-Crate community and the WorkflowHub Club.

Funding

European Commission Horizon 2020 (BioExcel-2 823830, EOSC-Life 824087), Horizon Europe (BY-COVID 101046203, FAIR-IMPACT 101057344).

Daniel Garijo is supported by the Madrid Government (Comunidad de Madrid-Spain) under the Multiannual Agreement with Universidad Politécnica de Madrid in the line Support for R&D projects for Beatriz Galindo researchers, in the context of the V PRICIT (Regional Programme of Research and Technological Innovation).

Leyla Jael Castro is supported by a German Research Foundation DFG grant for NFDI4DataScience.

Frederik Coppens is supported by Research Foundation - Flanders (FWO) for ELIXIR Belgium (I002819N).

Acknowledgements for Making Canonical Workflow Building Blocks

Section 5.1 is adapted from journal article published in Data Intelligence.

Published As

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth (2022):
Making Canonical Workflow Building Blocks interoperable across workflow languages.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00135

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Formatting as Markdown and LaTeX; figure caption formatting; references in s11 house style; citations merged and renumbered; acknowledgements and references moved to separate chapters. Fixed minor typos and grammatical errors.

Acknowledgements

This work has been done as part of the BioExcel CoE (https://www.bioexcel.eu/), a project funded by the European Union contracts H2020-INFRAEDI-02-2018 823830, H2020-EINFRA-2015-1 675728. Additional work is funded through EOSC-Life (https://www.eosc-life.eu/) contract H2020-INFRAEOSC-2018-2 824087, and ELIXIR-CONVERGE (https://elixir-europe.org/) contract H2020-INFRADEV-2019-2 871075.

The authors would also like to acknowledge contributions from: Felix Amaladoss, Cibin Sadasivan Baby, Finn Bacall, Rosa M. Badia, Sarah Butcher, Gerard Capes, Michael R. Crusoe, Alberto Eusebi, Carole Goble, Josep Lluís Gelpí, Modesto Orozco, Geoff Williams, Felix Amaladoss

Acknowledgements for The Specimen Data Refinery

Section 5.2 is adapted from a journal article published in Data Intelligence.

Published As

Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes (2022):
The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00134

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Formatting as Markdown and LaTeX; figures replaced with higher resolutions from source; figure caption formatting; references in s11 house style; added DOIs and URLs; cited preprints replaced with later publications citations merged and renumbered; funding and references moved to separate chapters. Fixed minor typos and grammatical errors.

Acknowledgements

This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement numbers 823827 (SYNTHESYS Plus), 871043 (DiSSCo Prepare), 823830 (BioExcel-2), 824087 (EOSC-Life).

Acknowledgements for Incrementally building FAIR Digital Objects

Section 5.3 is adapted from an abstract presented as poster by Stian Soiland-Reyes at First International Conference on FAIR Digital Objects (FDO2022) on 2022-08-26/–28 in Leiden, The Netherlands.

Published As

Oliver Woolland, Paul Brack, Stian Soiland-Reyes, Ben Scott, Laurence Livermore (2022):
Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e94349
https://doi.org/10.3897/rio.8.e94349

License and modifications

• License: Creative Commons Attribution License (CC BY 4.0).
• Modifications: Formatting as Markdown and LaTeX; references in s11 house style; added DOIs and URLs; funding and references moved to separate chapters; fixed minor typos and grammatical errors.

Acknowledgements

We acknowledge the SYNTHESYS+ and DiSSCO project members who have been invaluable in early evaluation and feedback on the development of SDR.

Funding

This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement numbers 823827 (SYNTHESYS Plus), 871043 (DiSSCo Prepare), 823830 (BioExcel-2), 824087 (EOSC-Life).